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RNA Biology Volume 13, 2016 - Issue 6
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Research Paper

Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors

Rodrigo D. RequiãoPrograma de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
,
Henrique José Araujo de SouzaPrograma de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
,
Silvana RossettoPrograma de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
,
Tatiana DomitrovicDepartamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
&
Fernando L. PalhanoPrograma de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BrazilCorrespondence[email protected]
Pages 561-568 | Received 01 Dec 2015, Accepted 25 Mar 2016, Published online: 12 May 2016

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Mariana H. Moreira, Géssica C. Barros, Rodrigo D. Requião, Silvana Rossetto, Tatiana Domitrovic & Fernando L. Palhano. (2019) From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli. RNA Biology 16:12, pages 1806-1816.
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Malgorzata J. Latallo, Shaopeng Wang, Daoyuan Dong, Blake Nelson, Nathan M. Livingston, Rong Wu, Ning Zhao, Timothy J. Stasevich, Michael C. Bassik, Shuying Sun & Bin Wu. (2023) Single-molecule imaging reveals distinct elongation and frameshifting dynamics between frames of expanded RNA repeats in C9ORF72-ALS/FTD. Nature Communications 14:1.
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Gemma E May, Christina Akirtava, Matthew Agar-Johnson, Jelena Micic, John Woolford & Joel McManus. (2023) Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning. eLife 12.
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Phillip C. Burke, Heungwon Park & Arvind Rasi Subramaniam. (2022) A nascent peptide code for translational control of mRNA stability in human cells. Nature Communications 13:1.
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Fabio Hedayioglu, Emma J Mead, Patrick B F O'Connor, Matas Skiotys, Owen J Sansom, Giovanna R Mallucci, Anne E Willis, Pavel V Baranov, C Mark Smales & Tobias von der Haar. (2022) Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles. Nucleic Acids Research 50:19, pages e112-e112.
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Alexandra Brakel, Andor Krizsan, Renke Itzenga, Carl N. Kraus, Laszlo OtvosJr.Jr. & Ralf Hoffmann. (2022) Influence of Substitutions in the Binding Motif of Proline-Rich Antimicrobial Peptide ARV-1502 on 70S Ribosome Binding and Antimicrobial Activity. International Journal of Molecular Sciences 23:6, pages 3150.
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Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close & Liesbet Geris. (2022) Ribosome exit tunnel electrostatics. Physical Review E 105:1.
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Yuhei Chadani, Nobuyuki Sugata, Tatsuya Niwa, Yosuke Ito, Shintaro Iwasaki & Hideki Taguchi. (2021) Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation. The EMBO Journal 40:23.
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Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch & Edward P. O’Brien. (2021) Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force. Biochemistry 60:43, pages 3223-3235.
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Puneet Sharma, Jie Wu, Benedikt S. Nilges & Sebastian A. Leidel. (2021) Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments. Nature Communications 12:1.
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Katarzyna Chyżyńska, Kornel Labun, Carl Jones, Sushma N Grellscheid & Eivind Valen. (2021) Deep conservation of ribosome stall sites across RNA processing genes. NAR Genomics and Bioinformatics 3:2.
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Géssica C. Barros, Rodrigo D. Requião, Rodolfo L. Carneiro, Claudio A. Masuda, Mariana H. Moreira, Silvana Rossetto, Tatiana Domitrovic & Fernando L. Palhano. (2021) Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex. Journal of Biological Chemistry 296, pages 100586.
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Emily Nicole Powers & Gloria Ann Brar. 2021. Ribosome Profiling. Ribosome Profiling 89 125 .
Nabeel Ahmed, Ulrike A. Friedrich, Pietro Sormanni, Prajwal Ciryam, Naomi S. Altman, Bernd Bukau, Günter Kramer & Edward P. O'Brien. (2020) Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates. Journal of Molecular Biology 432:24, pages 166696.
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Rodrigo D. Requião, Géssica C. Barros, Tatiana Domitrovic & Fernando L. Palhano. (2020) Influence of nascent polypeptide positive charges on translation dynamics. Biochemical Journal 477:15, pages 2921-2934.
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Cole S. SitronOnn Brandman. (2020) Detection and Degradation of Stalled Nascent Chains via Ribosome-Associated Quality Control. Annual Review of Biochemistry 89:1, pages 417-442.
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Slavica Pavlovic Djuranovic, Jessey Erath, Ryan J Andrews, Peter O Bayguinov, Joyce J Chung, Douglas L Chalker, James AJ Fitzpatrick, Walter N Moss, Pawel Szczesny & Sergej Djuranovic. (2020) Plasmodium falciparum translational machinery condones polyadenosine repeats. eLife 9.
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Marija Liutkute, Ekaterina Samatova & Marina V. Rodnina. (2020) Cotranslational Folding of Proteins on the Ribosome. Biomolecules 10:1, pages 97.
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Eva Maria Novoa, Irwin Jungreis, Olivier Jaillon & Manolis Kellis. (2019) Elucidation of Codon Usage Signatures across the Domains of Life. Molecular Biology and Evolution 36:10, pages 2328-2339.
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Ze Cheng & Gloria Ann Brar. (2019) Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs. Nucleic Acids Research 47:10, pages 5061-5073.
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Cole S. Sitron & Onn Brandman. (2019) CAT tails drive degradation of stalled polypeptides on and off the ribosome. Nature Structural & Molecular Biology 26:6, pages 450-459.
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Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike A. Friedrich, Günter Kramer & Edward P. O’Brien. (2019) A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data. PLOS Computational Biology 15:5, pages e1007070.
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Rodolfo L Carneiro, Rodrigo D Requião, Silvana Rossetto, Tatiana Domitrovic & Fernando L Palhano. (2019) Codon stabilization coefficient as a metric to gain insights into mRNA stability and codon bias and their relationships with translation. Nucleic Acids Research 47:5, pages 2216-2228.
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Guangying Ma, Xiaohua Shi, Qingcheng Zou, Danqing Tian, Xia An & Kaiyuan Zhu. (2018) iTRAQ-based quantitative proteomic analysis reveals dynamic changes during daylily flower senescence. Planta 248:4, pages 859-873.
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Serina M. Mazzoni-Putman & Anna N. Stepanova. (2018) A Plant Biologist’s Toolbox to Study Translation. Frontiers in Plant Science 9.
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Claudio A.P. Joazeiro. (2017) Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control. Annual Review of Cell and Developmental Biology 33:1, pages 343-368.
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Rodrigo D. Requião, Luiza Fernandes, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic & Fernando L. Palhano. (2017) Protein charge distribution in proteomes and its impact on translation. PLOS Computational Biology 13:5, pages e1005549.
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Cole S. Sitron, Joseph H. Park & Onn Brandman. (2017) Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation. RNA 23:5, pages 798-810.
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Nicholas R. Guydosh & Rachel Green. (2017) Translation of poly(A) tails leads to precise mRNA cleavage. RNA 23:5, pages 749-761.
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Dmitry E. Andreev, Patrick B. F. O'Connor, Gary Loughran, Sergey E. Dmitriev, Pavel V. Baranov & Ivan N. Shatsky. (2017) Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Research 45:2, pages 513-526.
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Guilhem Faure, Aleksey Y. Ogurtsov, Svetlana A. Shabalina & Eugene V. Koonin. (2016) Role of mRNA structure in the control of protein folding. Nucleic Acids Research 44:22, pages 10898-10911.
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